1IU3
| CRYSTAL STRUCTURE OF THE E.COLI SEQA PROTEIN COMPLEXED WITH HEMIMETHYLATED DNA | Descriptor: | 5'-D(*AP*AP*GP*GP*AP*TP*CP*CP*AP*A)-3', 5'-D(*TP*TP*GP*GP*AP*TP*CP*CP*TP*T)-3', SeqA protein | Authors: | Fujikawa, N, Kurumizaka, H, Nureki, O, Tanaka, Y, Yamazoe, M, Hiraga, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2002-02-26 | Release date: | 2003-06-17 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein. Nucleic Acids Res., 32, 2004
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1ITT
| Average Crystal Structure of (Pro-Pro-Gly)9 at 1.0 angstroms Resolution | Descriptor: | COLLAGEN TRIPLE HELIX | Authors: | Hongo, C, Nagarajan, V, Noguchi, K, Kamitori, S, Okuyama, K, Tanaka, Y, Nishino, N. | Deposit date: | 2002-02-03 | Release date: | 2003-02-03 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (1 Å) | Cite: | Average Crystal Structure of (Pro-Pro-Gly)9 at 1.0 angstroms Resolution Plym.J., 33, 2001
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1J3E
| Crystal Structure of the E.coli SeqA protein complexed with N6-methyladenine- guanine mismatch DNA | Descriptor: | 5'-D(*AP*AP*GP*GP*(6MA)P*TP*CP*CP*AP*A)-3', 5'-D(*TP*TP*GP*GP*AP*GP*CP*CP*TP*T)-3', SeqA protein | Authors: | Fujikawa, N, Kurumizaka, H, Nureki, O, Tanaka, Y, Yamazoe, M, Hiraga, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-01-24 | Release date: | 2004-05-18 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein Nucleic Acids Res., 32, 2004
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5DE0
| Dye-decolorizing protein from V. cholerae | Descriptor: | Deferrochelatase, PROTOPORPHYRIN IX CONTAINING FE | Authors: | Uchida, T, Sasaki, M, Tanaka, Y, Yao, M. | Deposit date: | 2015-08-25 | Release date: | 2015-10-21 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.24 Å) | Cite: | A Dye-Decolorizing Peroxidase from Vibrio cholerae. Biochemistry, 54, 2015
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6AIT
| Crystal structure of E. coli BepA | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Beta-barrel assembly-enhancing protease, ZINC ION | Authors: | Umar, M.S.M, Tanaka, Y, Kamikubo, H, Tsukazaki, T. | Deposit date: | 2018-08-24 | Release date: | 2018-12-26 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.598 Å) | Cite: | Structural Basis for the Function of the beta-Barrel Assembly-Enhancing Protease BepA. J. Mol. Biol., 431, 2019
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2D6Y
| Crystal Structure of transcriptional factor SCO4008 from Streptomyces coelicolor A3(2) | Descriptor: | L(+)-TARTARIC ACID, putative tetR family regulatory protein | Authors: | Hayashi, T, Tanaka, Y, Sakai, N, Yao, M, Tamura, T, Tanaka, I. | Deposit date: | 2005-11-15 | Release date: | 2006-10-31 | Last modified: | 2013-09-04 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | SCO4008, a Putative TetR Transcriptional Repressor from Streptomyces coelicolor A3(2), Regulates Transcription of sco4007 by Multidrug Recognition. J.Mol.Biol., 425, 2013
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2DG7
| Crystal structure of the putative transcriptional regulator SCO0337 from Streptomyces coelicolor A3(2) | Descriptor: | putative transcriptional regulator | Authors: | Hayashi, T, Tanaka, Y, Sakai, N, Yao, M, Tamura, T, Tanaka, I. | Deposit date: | 2006-03-08 | Release date: | 2007-03-13 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Crystal structure of the putative transcriptional regulator SCO0337 from Streptomyces coelicolor A3(2) To be Published
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2DG6
| Crystal structure of the putative transcriptional regulator SCO5550 from Streptomyces coelicolor A3(2) | Descriptor: | putative transcriptional regulator | Authors: | Hayashi, T, Tanaka, Y, Sakai, N, Yao, M, Tamura, T, Tanaka, I. | Deposit date: | 2006-03-08 | Release date: | 2007-03-13 | Last modified: | 2018-03-28 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Structural and genomic DNA analysis of a putative transcription factor SCO5550 from Streptomyces coelicolor A3(2): regulating the expression of gene sco5551 as a transcriptional activator with a novel dimer shape Biochem. Biophys. Res. Commun., 435, 2013
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2EL2
| Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 (L185M) | Descriptor: | S-ADENOSYL-L-HOMOCYSTEINE, SODIUM ION, diphthine synthase | Authors: | Asada, Y, Tanaka, Y, Pampa, K, Matsuura, Y, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2007-03-26 | Release date: | 2007-10-02 | Last modified: | 2021-11-10 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 (L185M) To be Published
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2E7D
| Crystal structure of a NEAT domain from Staphylococcus aureus | Descriptor: | ACETATE ION, GLYCEROL, Hypothetical protein IsdH, ... | Authors: | Suenaga, A, Tanaka, Y, Yao, M, Kumagai, I, Tanaka, I, Tsumoto, K. | Deposit date: | 2007-01-09 | Release date: | 2008-01-22 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Structural basis for multimeric heme complexation through a specific protein-heme interaction: the case of the third neat domain of IsdH from Staphylococcus aureus J.Biol.Chem., 283, 2008
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2EK2
| Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 (E140M) | Descriptor: | S-ADENOSYL-L-HOMOCYSTEINE, SODIUM ION, diphthine synthase | Authors: | Asada, Y, Matsuura, Y, Tanaka, Y, Nakamoto, T, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2007-03-22 | Release date: | 2007-09-25 | Last modified: | 2021-11-10 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 (E140M) To be Published
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2EKB
| Structural study of Project ID TTHB049 from Thermus thermophilus HB8 (L19M) | Descriptor: | Alpha-ribazole-5'-phosphate phosphatase, SODIUM ION | Authors: | Asada, Y, Taketa, M, Tanaka, Y, Matsuura, Y, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2007-03-22 | Release date: | 2007-09-25 | Last modified: | 2021-11-10 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Structural study of Project ID TTHB049 from Thermus thermophilus HB8 (L19M) To be Published
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2YVX
| Crystal structure of magnesium transporter MgtE | Descriptor: | MAGNESIUM ION, Mg2+ transporter MgtE | Authors: | Hattori, M, Tanaka, Y, Fukai, S, Ishitani, R, Nureki, O. | Deposit date: | 2007-04-18 | Release date: | 2007-09-04 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (3.5 Å) | Cite: | Crystal structure of the MgtE Mg(2+) transporter Nature, 448, 2007
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2YVZ
| Crystal structure of magnesium transporter MgtE cytosolic domain, Mg2+-free form | Descriptor: | Mg2+ transporter MgtE | Authors: | Hattori, M, Tanaka, Y, Fukai, S, Ishitani, R, Nureki, O. | Deposit date: | 2007-04-18 | Release date: | 2007-09-04 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (3.9 Å) | Cite: | Crystal structure of the MgtE Mg(2+) transporter Nature, 448, 2007
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2YVY
| Crystal structure of magnesium transporter MgtE cytosolic domain, Mg2+ bound form | Descriptor: | MAGNESIUM ION, Mg2+ transporter MgtE | Authors: | Hattori, M, Tanaka, Y, Fukai, S, Ishitani, R, Nureki, O. | Deposit date: | 2007-04-18 | Release date: | 2007-09-04 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Crystal structure of the MgtE Mg(2+) transporter Nature, 448, 2007
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2Z92
| Crystal structure of the Fab fragment of anti-ciguatoxin antibody 10C9 in complex with CTX3C_ABCDE | Descriptor: | (4Z)-2,8:7,12:11,15:14,18:17,22-PENTAANHYDRO-4,5,6,9,10,13,19,20,21-NONADEOXY-D-ARABINO-D-ALLO-D-ALLO-DOCOSA-4,9,20-TRIENITOL, Anti-ciguatoxin antibody 10C9 Fab heavy chain, Anti-ciguatoxin antibody 10C9 Fab light chain, ... | Authors: | Ui, M, Tanaka, Y, Tsumoto, K. | Deposit date: | 2007-09-14 | Release date: | 2008-05-06 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | How Protein Recognizes Ladder-like Polycyclic Ethers: INTERACTIONS BETWEEN CIGUATOXIN (CTX3C) FRAGMENTS AND ITS SPECIFIC ANTIBODY 10C9 J.Biol.Chem., 283, 2008
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2Z93
| Crystal structure of Fab fragment of anti-ciguatoxin antibody 10C9 in complex with CTX3C-ABCD | Descriptor: | 1,6:5,9:8,12:11,16-TETRAANHYDRO-2,3,4,10,13,14-HEXADEOXY-D-GLYCERO-D-ALLO-D-GULO-HEPTADECA-2,13-DIENITOL, Anti-ciguatoxin antibody 10C9 Fab heavy chain, Anti-ciguatoxin antibody 10C9 Fab light chain | Authors: | Ui, M, Tanaka, Y, Tsumoto, K. | Deposit date: | 2007-09-14 | Release date: | 2008-05-06 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | How Protein Recognizes Ladder-like Polycyclic Ethers: INTERACTIONS BETWEEN CIGUATOXIN (CTX3C) FRAGMENTS AND ITS SPECIFIC ANTIBODY 10C9 J.Biol.Chem., 283, 2008
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2Z91
| Crystal structure of the Fab fragment of anti-ciguatoxin antibody 10C9 | Descriptor: | Anti-ciguatoxin antibody 10C9 FAB heavy chain, Anti-ciguatoxin antibody 10C9 FAB light chain | Authors: | Ui, M, Tanaka, Y, Tsumoto, K. | Deposit date: | 2007-09-14 | Release date: | 2008-05-06 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | How Protein Recognizes Ladder-like Polycyclic Ethers: INTERACTIONS BETWEEN CIGUATOXIN (CTX3C) FRAGMENTS AND ITS SPECIFIC ANTIBODY 10C9 J.Biol.Chem., 283, 2008
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3A0A
| Structure of (PPG)4-OPG-(PPG)4, monoclinic, twinned crystal | Descriptor: | collagen-like peptide | Authors: | Okuyama, K, Morimoto, T, Hongo, C, Katagiri, A, Tanaka, Y, Nishino, N. | Deposit date: | 2009-03-13 | Release date: | 2010-03-09 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.36 Å) | Cite: | Crystal structure of (PPG)4-OPG-(PPG)4 To be Published
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2ZZT
| Crystal structure of the cytosolic domain of the cation diffusion facilitator family protein | Descriptor: | Putative uncharacterized protein, SULFATE ION | Authors: | Higuchi, T, Hattori, M, Tanaka, Y, Ishitani, R, Nureki, O. | Deposit date: | 2009-02-25 | Release date: | 2009-08-18 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.842 Å) | Cite: | Crystal structure of the cytosolic domain of the cation diffusion facilitator family protein Proteins, 76, 2009
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6KX0
| Crystal structure of SN-101 mAb non-liganded form | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Fab Fragment-SN-101-Heavy chain, Fab Fragment-SN-101-Light chain | Authors: | Wakui, H, Tanaka, Y, Kato, K, Ose, T, Matsumoto, I, Min, Y, Tachibana, T, Nishimura, S.-I. | Deposit date: | 2019-09-09 | Release date: | 2020-07-29 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.404 Å) | Cite: | A straightforward approach to antibodies recognising cancer specific glycopeptidic neoepitopes Chem Sci, 11, 2020
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6KX1
| Crystal structure of SN-101 mAb in complex with MUC1 glycopeptide | Descriptor: | 2-acetamido-2-deoxy-alpha-D-galactopyranose, Fab Fragment-SN-101-Heavy chain, Fab Fragment-SN-101-Light chain, ... | Authors: | Wakui, H, Tanaka, Y, Kato, K, Ose, T, Matsumoto, I, Min, Y, Tachibana, T, Nishimura, S.-I. | Deposit date: | 2019-09-09 | Release date: | 2020-07-29 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.773 Å) | Cite: | A straightforward approach to antibodies recognising cancer specific glycopeptidic neoepitopes Chem Sci, 11, 2020
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2E8H
| Crystal structure of PH0725 from Pyrococcus horikoshii OT3 | Descriptor: | Probable diphthine synthase, S-ADENOSYL-L-HOMOCYSTEINE, SODIUM ION | Authors: | Sugahara, M, Taketa, M, Tanaka, Y, Matsuura, Y, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2007-01-19 | Release date: | 2007-07-24 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Crystal structure of PH0725 from Pyrococcus horikoshii OT3 To be Published
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2E27
| Crystal structure of Fv fragment of anti-ciguatoxin antibody complexed with ABC-ring of ciguatoxin | Descriptor: | 3,7:6,10:9,14-TRIANHYDRO-2,5,11,12,13-PENTADEOXY-4-O-(METHOXYMETHYL)-L-ARABINO-L-ALLO-TETRADEC-12-ENONIC ACID, DIMETHYL SULFOXIDE, GLYCEROL, ... | Authors: | Yokota, A, Tanaka, Y, Tsumoto, K. | Deposit date: | 2006-11-08 | Release date: | 2007-11-13 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Critical contribution of aromatic rings to specific recognition of polyether rings. The case of ciguatoxin CTX3C-ABC and its specific antibody 1C49. J.Biol.Chem., 283, 2008
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3BIK
| Crystal Structure of the PD-1/PD-L1 Complex | Descriptor: | GLYCEROL, Programmed cell death 1 ligand 1, Programmed cell death protein 1 | Authors: | Lin, D.Y, Tanaka, Y, Iwasaki, M, Gittis, A.G, Su, H.P, Mikami, B, Okazaki, T, Honjo, T, Minato, N, Garboczi, D.N. | Deposit date: | 2007-11-30 | Release date: | 2008-02-26 | Last modified: | 2023-08-30 | Method: | X-RAY DIFFRACTION (2.65 Å) | Cite: | The PD-1/PD-L1 complex resembles the antigen-binding Fv domains of antibodies and T cell receptors. Proc.Natl.Acad.Sci.Usa, 105, 2008
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